Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013843687.1 DESRU_RS18845 ornithine--oxo-acid transaminase
Query= curated2:O27392 (390 letters) >NCBI__GCF_000215085.1:WP_013843687.1 Length = 396 Score = 292 bits (748), Expect = 1e-83 Identities = 152/388 (39%), Positives = 230/388 (59%), Gaps = 11/388 (2%) Query: 3 SEEIIELERKFIMQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVAL 62 S IIE + Y PIV++ +G V D EGN Y+D + + + GH HPK+ Sbjct: 4 SNNIIEKTEALGARNYHPLPIVIAKAEGVWVEDPEGNRYMDMLSAYSALNQGHRHPKIIK 63 Query: 63 AICHQAQRLIHSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKFT-- 120 A+ QA ++ +S ++ + + L ++ +R+ N+GAEA E A+K R++ Sbjct: 64 ALKDQADKVTLTSRAFHNDQLYRFYEKLAQVTGKNRILPMNTGAEAVETAVKAIRRWAYD 123 Query: 121 ------GKSEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDIGAMADAV 174 ++EII +FHGRT + + +++Y F P GFK +PYGD A+ A+ Sbjct: 124 RKKVVENQAEIIVCRGNFHGRTTTITSFSSEEEYKRGFGPFTPGFKIIPYGDTEALKGAI 183 Query: 175 GDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFASQL 234 TAA +LEP+QGE G++IP EG+L++ + ++N++L + DE+QTGFGRTG FA Sbjct: 184 MPNTAAFLLEPIQGEAGIVIPREGFLQEAYAICKENNLLFVADEIQTGFGRTGRWFACDW 243 Query: 235 FGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCAAAIATIEVL 293 GV PDI + KA+GGG PI AV A+E + FEPG HGSTFGGNP CA A+A +EVL Sbjct: 244 EGVVPDIYIMGKALGGGVLPISAVAADEDILGVFEPGSHGSTFGGNPLACAVAVAALEVL 303 Query: 294 MDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGECAGVVDAAREMGV 353 +E LP+++ +G YF+ +L+Q+ + +++IRG GL IG+E++ E + +EM + Sbjct: 304 EEENLPQQSLTLGEYFMNQLKQIKN--PVIKEIRGKGLFIGLELNTEARPYCEKLKEMKL 361 Query: 354 LINCTAGKVIRIVPPLVIKKEEIDAAVD 381 L T IR PPL I +EE+D A + Sbjct: 362 LCKETHVHTIRFAPPLTITREELDWAYE 389 Lambda K H 0.320 0.138 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 383 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 390 Length of database: 396 Length adjustment: 31 Effective length of query: 359 Effective length of database: 365 Effective search space: 131035 Effective search space used: 131035 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory